Pokémon Yellow been put onto the Nintendo 3DS Virtual Console and have largely remained unaltered including glitches, , however unlike the other Virtual Console games, this game comes with a variety of alterations. In addition to this, it does not allow for the Virtual Console features of Save Backups or Restore Points. It also uses the X Button to bring up the pause menu like the 3DS games, rather than bringing up the Virtual Console menu.

Wireless Trading

The most notable addition of the Virtual Console titles are the inclusion of Wireless Battle & Trade features. When you go to the Cable Club in each Pokémon Center, the game will run as normal but will activate a Virtual Console feature that will ask you to search for or join another player's game. From there, the general Cable Club features continue as normal. However, if you break the wireless connection, the features will end.

Move Animations

Since 1996, various changes have been applied to how games can utilise flashing screens. This is due to the effect that these flashing animations can have on people with photo-sensitive epilepsy. As such, for the Virtual Console releases, various moves have had updated animations in order to attempt to dull the effect of rapid flashing which could potentially trigger these things.

A change exclusive to Pokémon Yellow in the west, and not Pokémon Pikachu in Japan, is the alteration of the sprite for the Pokémon Jynx. Back in the early 2000s, Jynx had a redesign with its face being changed from black to purple and the sprite for Pokémon Yellow has been adapted to reflect this change. The interesting thing about this change is that it makes Jynx's sprite have more colours than any other sprite in the game.

Since there is no Virtual Console release of Pokémon Stadium on the Wii U for the Virtual Console titles to connect with, there would be no way in order to play this game. However, in the Virtual Console release, you can play this game without having a Pikachu with Surf, you just need your Pikachu in your party and you can play the game.